{"id":"W4409710424","doi":"10.3389/fbinf.2025.1574359","title":"Artificial intelligence in variant calling: a review","year":2025,"lang":"en","type":"review","venue":"Frontiers in Bioinformatics","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":25,"is_retracted":false,"has_abstract":true,"ca_institutions":"Université Laval","funders":"Genome Canada","keywords":"Indel; Genomics; Computer science; Artificial intelligence; Scalability; Computational biology; DNA sequencing; Data science; Single-nucleotide polymorphism; Biology; Genetics; Genome; Gene","routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.001780149,0.001059612,0.00172442,0.003124403,0.0003269073,0.001605113,0.001541499,0.001597046,0.00406083],"category_scores_gemma":[0.003607937,0.0004734189,0.001041062,0.00440771,0.0008483402,0.0020519,0.0008534107,0.002122311,0.002217968],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0008667322,"about_ca_system_score_gemma":0.002053866,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002142809,"about_ca_topic_score_gemma":0.002286006,"domain_scores_codex":[0.9994524,0.0001441935,0.00009238275,0.0001048657,0.0001729785,0.00003314026],"domain_scores_gemma":[0.996823,0.002523319,0.0001695122,0.00006117998,0.0003483806,0.00007461231],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"not_applicable","study_design_scores_codex":[0.00004815382,0.00004915004,0.0002174649,0.02453401,0.0001628572,0.0001222795,0.00006517884,0.0007450745,0.0004916284,0.006090982,0.02124599,0.9462273],"study_design_scores_gemma":[0.00002138796,0.00009743029,0.0008877731,0.01252886,0.0003009881,0.001031118,0.00007079847,0.0003418506,0.0004812304,0.007175679,0.9770089,0.00005404742],"study_design_candidate":"not_applicable","study_design_consensus":null,"genre_codex":"review","genre_gemma":"review","genre_scores_codex":[0.00005870975,0.9983363,0.0004621338,0.0003531539,0.0001549407,0.000005834524,0.00002587658,0.00001165042,0.0005915479],"genre_scores_gemma":[0.0004440746,0.998247,0.0006621028,0.0002369712,0.0001621913,0.000009644188,0.00004490179,0.000003961316,0.0001890791],"genre_candidate":"review","genre_consensus":"review","teacher_disagreement_score":0.00406083,"threshold_uncertainty_score":0.01358485,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02845797252138531,"score_gpt":0.3034648592879921,"score_spread":0.2750068867666067,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). Scores rank; they never assert a category."}}